A5051290724- Gut microbiota and health
- Genetic Associations and Epidemiology
- Epigenetics and DNA Methylation
- Urinary Tract Infections Management
- Genetic Syndromes and Imprinting
- Metabolomics and Mass Spectrometry Studies
- Diet and metabolism studies
- Reproductive tract infections research
- Pelvic floor disorders treatments
- Mental Health Research Topics
- Nutritional Studies and Diet
- Meta-analysis and systematic reviews
- Microbial Community Ecology and Physiology
- Impact of Technology on Adolescents
- Genomics and Phylogenetic Studies
- Advanced Chemical Sensor Technologies
- Emotion and Mood Recognition
- Adipose Tissue and Metabolism
- Probiotics and Fermented Foods
- Breastfeeding Practices and Influences
- Infant Nutrition and Health
- Reliability and Agreement in Measurement
- Digital Mental Health Interventions
- Genetic and phenotypic traits in livestock
- Evolution and Genetic Dynamics
Courant Institute of Mathematical Sciences
2024
Rockefeller University
2019-2024
University of California, Los Angeles
2017-2024
New York University
2023-2024
Tel Aviv University
2016-2018
Exact Sciences (United States)
2016
Tel Aviv Sourasky Medical Center
2016
Abstract How complex communities assemble through the animal’s life, and how predictable process is remains unexplored. Here, we investigate forces that drive assembly of rumen microbiomes throughout a cow’s with emphasis on balance between stochastic deterministic processes. We analyse development microbiome from birth to adulthood using 16S-rRNA amplicon sequencing data find animals shared group core successional species invaded early persisted until adulthood. Along factors, such as age...
Abstract Microbial breakdown of organic matter is one the most important processes on Earth, yet controls decomposition are poorly understood. Here we track 36 terrestrial human cadavers in three locations and show that a phylogenetically distinct, interdomain microbial network assembles during despite selection effects location, climate season. We generated metagenome-assembled genome library from cadaver-associated soils integrated it with metabolomics data to identify links between...
Genetic data are known to harbor information about human demographics, and genotyping commonly used for capturing ancestry by leveraging genome-wide differences between populations. In contrast, it is not clear what extent population structure captured whole-genome DNA methylation data. We demonstrate, using three large-cohort 450K array sets, that signal mirrored in can be further isolated more effectively the correlation of CpGs with cis-located SNPs. Based on these insights, we propose a...
Abstract Preterm birth (PTB) is the leading cause of neonatal morbidity and mortality. The vaginal microbiome has been associated with PTB, yet mechanisms underlying this association are not fully understood. Understanding microbial genetic adaptations to selective pressures, especially those related host, may yield insights into these associations. Here, we analyze metagenomic data from 705 samples collected during pregnancy 40 women who delivered preterm spontaneously 135 term controls...
Abstract Over the last ten years, there has been considerable progress in using digital behavioral phenotypes, captured passively and continuously from smartphones wearable devices, to infer depressive mood. However, most phenotype studies suffer poor replicability, often fail detect clinically relevant events, use measures of depression that are not validated or suitable for collecting large longitudinal data. Here, we report high-quality assessments mood computerized adaptive testing...
Dynamic changes in microbial communities play an important role human health and disease. Specifically, deciphering how species a community interact with each other their environment can elucidate mechanisms of disease, problem typically investigated using tools from ecology. Yet, such methods require measurements absolute densities, whereas typical datasets only provide estimates relative abundances. Here, we systematically investigate models dynamics the simplex We derive new nonlinear...
Maximizing elements for your genome The accumulation of mutations is typically limited by selective parameters. One such parameter the needed to build proteins and molecules maintain cells. Examining underlying carbon, oxygen, nitrogen content different amino acids, Shenhav et al. examined pressure resulting from nutrient limitation (see Perspective Polz Cordero). authors identified “resource-driven” selection as a purifying force associated with environmental availability, particularly...
Alzheimer's disease (AD) is influenced by a variety of modifiable risk factors, including person's dietary habits. While the ketogenic diet (KD) holds promise in reducing metabolic risks and potentially affecting AD progression, only few studies have explored KD's impact, especially on blood cerebrospinal fluid (CSF). Our study involved participants at for AD, either cognitively normal or with mild cognitive impairment. The consumed both modified Mediterranean Ketogenic Diet (MMKD) American...
Abstract Summary GLINT is a user-friendly command-line toolset for fast analysis of genome-wide DNA methylation data generated using the Illumina human arrays. GLINT, which does not require any programming proficiency, allows an easy execution Epigenome-Wide Association Study pipeline under different models while accounting known confounders in data. Availability and Implementation software, freely available at https://github.com/cozygene/glint/releases. It requires Python 2.7 several...
Given the highly dynamic and complex nature of human gut microbial community, ability to identify predict time-dependent compositional patterns microbes is crucial our understanding structure functions this ecosystem. One factor that could affect such interactions, wherein community composition at a given time point affects later point. However, field has not yet settled on degree effect. Specifically, it been recently suggested only minority taxa depend in earlier times. To address issue...
We introduce a Bayesian semi-supervised method for estimating cell counts from DNA methylation by leveraging an easily obtainable prior knowledge on the cell-type composition distribution of studied tissue. show mathematically and empirically that alternative methods which attempt to infer without reference only capture linear combinations rather than provide one component per type. Our approach allows construction components such each corresponds single type, provides new opportunity...
A large proportion of Depression Disorder patients do not receive an effective diagnosis, which makes it necessary to find a more objective assessment facilitate rapid and accurate diagnosis depression. Speech data is easy acquire clinically, its association with depression has been studied, although the actual predictive effect voice features examined. Thus, we have general understanding extent contribute identification In this study, investigated significance between using binary logistic...
Microbiome data analysis can be difficult because of particular features, some unavoidable and due to technical limitations DNA sequencing instruments. The first step in many analyses that ultimately reveals patterns similarities differences among sets samples (e.g., separating from sick healthy people or seawater versus soil) is calculating the difference between each pair samples.
Longitudinal studies are crucial for understanding complex microbiome dynamics and their link to health. We introduce TEMPoral TEnsor Decomposition (TEMPTED), a time-informed dimensionality reduction method high-dimensional longitudinal data that treats time as continuous variable, effectively characterizing temporal information handling varying sampling. TEMPTED captures key microbial dynamics, facilitates beta-diversity analysis, enhances reproducibility by transferring learned...
Systematic reviews and meta-analyses are important tools for synthesizing evidence from multiple studies. They serve to increase power improve precision, in the same way that large studies can do, but also establish consistency of effects replicability results across In this work we propose statistical quantify effect signs (or directions) their consistency. We suggest these accompany fixed-effect or random-effects meta-analysis, show they convey information assessment intervention under...
Abstract Longitudinal studies are crucial for understanding complex microbiome dynamics and their link to health. We introduce TEMPoral TEnsor Decomposition (TEMPTED), a time-informed dimensionality reduction method high-dimensional longitudinal data that treats time as continuous variable, effectively characterizing temporal information handling varying sampling. TEMPTED captures key microbial dynamics, facilitates beta-diversity analysis, enhances reproducibility by transferring learned...
Abstract Longitudinal studies of microbial communities have emphasized that host-associated microbiota are highly dynamic as well underscoring the potential biomedical relevance understanding these dynamics. Despite this increasing appreciation, statistical challenges in design and analysis longitudinal microbiome such sequence counting, technical variation, signal aliasing, contamination, sparsity, missing data, algorithmic scalability remain. In review we discuss highlight current progress...